tbuckley/cabot-search huggingface dataset:
Abstract B024: Phosphoinositide focused CRISPR screen reveals ITGAV as a critical gene in pancreatic cancer growth and invasion
Authors: Daniel K.C. Lee, Ryan Loke, Lydia To, Keyue Chen, Jonathan T.S. Chow, Leonardo Salmena
Journal: Cancer Research (2022)

Abstract Background: Pancreatic Cancer (PC) is one of the most aggressive cancer types, with less than 10% of patients surviving at 5-years. One hallmark of PC is the frequent mutation of the oncogene KRAS resulting in the constitutive activation of the phosphoinositide-3-kinase (PI3K) signaling pathway. The PI3K pathway is an intracellular signaling pathway that regulates cell growth, metabolism, and survival in response to extracellular signals. Given the importance of deregulated phosphoinositide (PI) signaling in PC, we hypothesize that genes coding for PI-metabolizing enzymes and effectors may have significant and unappreciated roles in PC. Methods: We generated a CRISPR knockout (KO) library that targets 1,534 PI-associated genes to discover novel essential genes in PC. Results: In a PANC-1 screen, we identified 106 essential genes across all timepoints, including 28 novel candidate genes and 78 previously identified essential genes. Among six validated candidate genes, we demonstrate that Integrin Subunit Alpha V (ITGAV) is a protein with clinical importance in PC. Treatment of PC cell lines with an ITGAV integrin antagonist as well as KO of ITGAV resulted in reduced cancer associated phenotypes in vitro, including reduced proliferation rate and compromised migration and invasion capacity. Ongoing studies will investigate perturbations in signaling pathways associated with ITGAV, and aim to elucidate roles for ITGAV in metastatic progression and therapy response. Conclusions: Overall, these findings indicate that ITGAV inhibition represents a putative strategy for the treatment of PC. Citation Format: Daniel K.C. Lee, Ryan Loke, Lydia To, Keyue Chen, Jonathan T.S. Chow, Leonardo Salmena. Phosphoinositide focused CRISPR screen reveals ITGAV as a critical gene in pancreatic cancer growth and invasion [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B024.
Abstract PR009: An epigenetic memory of inflammation controls context-dependent lineage plasticity in the pancreas
Authors: David J. Falvo, Adrien Grimont, Paul Zumbo, Julie L. Yang, Alexa Osterhoudt, Grace Pan, Andre F. Rendeiro, John E. Wilkinson, Friederike Dündar, Olivier Elemento, Rhonda K. Yantiss, Doron Betel, Richard Koch, Rohit Chandwani
Journal: Cancer Research (2022)

Abstract Inflammation is essential to the disruption of tissue homeostasis, and, in the pancreas, can destabilize the identity of terminally differentiated acinar cells. A longstanding question has been whether a history of past injuries instructs subsequent homeostatic responses to future stimuli – despite being distantly separated in time. Thus, we employ here Mist1-CreERT2; LSL-tdTomato lineage-tracing mice to investigate the long-term effects of a transient inflammatory episode on pancreatic tissue homeostasis. We delineate the chromatin dynamics that accompany the cycle of metaplasia and regeneration following pancreatitis, and reveal that the pancreatic acinar cell compartment durably retains specific inflammation-induced epigenetic changes even 18-weeks after exposure to the original inflammatory stimulus. We observe that despite histologic resolution of pancreatitis, acinar cells fail to return to their molecular baseline after several months, representing an incomplete cell fate decision. Motif analysis demonstrates the enrichment of AP-1/Fra1 motifs at these persistently accessible memory regions—a transcriptional effector activated downstream of the Ras/MAPK pathway. This epigenetic memory controls lineage plasticity, with diminished metaplasia in response to a second inflammatory insult but increased tumorigenesis with an oncogenic Kras mutation. We demonstrate that pancreatic acinar cells exhibit rapid malignant transformation upon re-challenge with oncogenic stress via inflammatory memory recall, with robust reactivation of genes associated with differentially accessible memory regions. Together, our findings define the dynamics and recall of an epigenetic memory of inflammation that impacts cell fate decisions in a context-dependent manner. Citation Format: David J. Falvo, Adrien Grimont, Paul Zumbo, Julie L. Yang, Alexa Osterhoudt, Grace Pan, Andre F. Rendeiro, John E. Wilkinson, Friederike Dündar, Olivier Elemento, Rhonda K. Yantiss, Doron Betel, Richard Koch, Rohit Chandwani. An epigenetic memory of inflammation controls context-dependent lineage plasticity in the pancreas [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr PR009.
Abstract C006: Loss of the MGAT5 glycosyltransferase sensitizes pancreatic tumor cells to immune clearance
Authors: Erin Hollander, Ben Stanger
Journal: Cancer Research (2022)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is currently the third leading cause of cancer-related death in the United States. The five-year survival rate of less than nine percent is attributed mainly to a difficulty in early detection and a lack of effective treatments. Tumor-associated glycans represent a potential anti-tumor target for two reasons: (i) protein glycosylation is known to play a role in tumor progression, and (ii) alternatively glycosylated proteins may function as tumor neoantigens. The glycosyltransferase MGAT5 catalyzes the formation of beta-1,6-N-acetylglucosamine branched glycans, and overexpression has been implicated in tumor growth and metastasis in multiple cancers. Using a panel of clonal cell lines that recapitulate the immune heterogeneity of PDAC, we found that knockout of MGAT5 in some clones (“T cell-inflamed" tumors) allows for complete clearance of tumors while in other clones (“non-T cell-inflamed”) MGAT5 deficiency led to a marked decrease in tumor growth. This phenotype was confirmed in orthotopic injection as well as subcutaneous injection into syngeneic mice. By contrast, MGAT5 loss had no impact on tumor cell growth in vitro. To probe immune system involvement in this robust rejection of tumor growth, the MGAT5 KO cells were injected into Nod/Scid mice, resulting in full rescue of the phenotype. Tumor eradication or growth inhibition in vivo was found to be dependent specifically on the presence of CD4/CD8 T cells and dendritic cells. Tumor challenge experiments, in which mice were immunized with MGAT5 KO cells and challenged with wild-type tumors four weeks later, revealed that tumor rejection was associated with a durable immunologic memory. Finally, therapeutic vaccination with the knockout line concomitantly with wild-type tumor cell injection led to decreased tumor growth. These results are consistent with a model in which MGAT5 loss results in the formation of new tumor antigens and/or enhances the immunogenicity of pre-existing antigens. Ongoing work seeks to determine the identity of the responsible antigens and further investigate the relationship between altered glycosylation and anti-tumor immunity. Citation Format: Erin Hollander, Ben Stanger. Loss of the MGAT5 glycosyltransferase sensitizes pancreatic tumor cells to immune clearance [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr C006.
Abstract A068: Investigation of changes in epithelial cell states in pancreatic cancer using human organoids
Authors: Ling Huang, Senthil Muthuswamy
Journal: Cancer Research (2022)

Abstract Pancreatic cancer is among the deadliest cancers in the US. The low survival rates of pancreatic cancer are mainly due to late diagnosis and a lack of effective treatments. To improve the clinical management of pancreatic cancer, we need better understand the biological mechanisms underlying the initiation and progression of this disease. With a focus on elucidating pancreatic cancer biology in human patients, we have developed organoid models for pancreatic normal physiology and malignancy using pluripotent stem cells or patient tumor tissues. Using stem cell-derived organoids, we investigated the interactions between pancreatic epithelial cell states, oncogenic signaling pathways, and cytokines. In this study, we discovered that human acinar organoids, compared to ductal organoids, were more sensitive to KRasG12D oncogenic signaling in vitro and in vivo, which supported acinar cells as the main cell of origin for pancreatic cancer in human patients. We have also developed working pipelines using organoid models to identify biomarkers and predict patient drug responses. Based on those successful studies, we now focus on investigating biological principles underlying racial disparities in pancreatic cancer using human cell models. Citation Format: Ling Huang, Senthil Muthuswamy. Investigation of changes in epithelial cell states in pancreatic cancer using human organoids [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A068.
Abstract B070: Deletion of NEMO inhibits PanIN development but accelerates PanIN progression towards PDAC
Authors: Miltiadis Tsesmelis, Melanie Gerstenlauer, Uta Manfras, Thomas F.E. Barth, Harald Jakob Maier, Lap Kwan Chan, Thomas Wirth
Journal: Cancer Research (2022)

Abstract Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest types of cancer with a 5-year survival rate of less than 10%. Importantly, the canonical NF-κB pathway, which regulates critical cellular functions including inflammation, is active in the majority of PDAC cases as well as in pancreatic intraepithelial neoplasias (PanINs). Our study investigated the role of NF-κB signaling in the development and progression of PanINs and PDAC by deleting NF-κB essential modulator (NEMO), an essential protein for the activation of the NF-κB pathway. We used genetically-modified mice with pancreas-specific expression of oncogenic KRAS (KC mouse model). To blunt the canonical NF-κB pathway, KC mice were crossed to NEMO-floxed mice, allowing pancreas-specific deletion of NEMO (KNeC mouse model). The mice were injected with cerulein to promote the development of pancreatitis and accelerate the development of PDAC. Analysis of the pancreata at the time point of 8 weeks revealed that NEMO deletion reduced the infiltration of immune cells and the collagen deposition in the pancreas. However, no significant difference in the number of PanINs between the KC and KNeC mice was observed. In contrast, analysis at the time point of 10 months demonstrated that NEMO deletion drastically reduced the total number of PanINs and the field covered by desmoplasia. In addition, KNeC pancreata exhibited reduced inflammation compared to KC pancreata. Strikingly, however, NEMO deletion accelerated the progression of low-grade to high-grade PanINs and eventually to PDAC and reduced the lifespan of the mice. Mechanistically, NEMO deletion blocked the oncogene-induced senescence (OIS) that is active in low-grade PanINs. RNA-seq analysis revealed that inhibition of OIS resulted in reduced expression of the senescence-associated secretory phenotype (SASP). Finally, NEMO deletion increased the proliferation rate and the accumulation of DNA damage in precancerous lesion cells, supporting their progression to high-grade PanINs. Collectively, our study gives a mechanistic insight of the role of NF-κB in the development and progression of precancerous lesions. It underscores that NEMO exerts oncogene properties by supporting the development of new low-grade PanINs, but at the same time, it exerts tumor-suppressor properties by maintaining OIS in PanINs. Citation Format: Miltiadis Tsesmelis, Melanie Gerstenlauer, Uta Manfras, Thomas F.E. Barth, Harald Jakob Maier, Lap Kwan Chan, Thomas Wirth. Deletion of NEMO inhibits PanIN development but accelerates PanIN progression towards PDAC [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B070.
Abstract IA016: Determinants of B cell fate and function in cancer
Authors: Yuliya Pylayeva-Gupta
Journal: Cancer Research (2022)

Abstract Effector B cell responses in solid malignancies are associated with anti-tumor immunity and favorable response to immunotherapy. B cells can amplify anti-tumor immune responses through antibody production, antigen presentation, and pro-inflammatory cytokine release; yet B cells in cancer patients and tumor-bearing mice often fail to support these effector cell functions. The determinants of B cell fate and function in cancer are still not clear. We find that systemic exposure to STING agonists potentiates expansion of immunosuppressive regulatory human and mouse IL-35+ B lymphocytes in an IRF3 dependent manner. Mechanistically, the loss of STING signaling in B cells or treatment with cGAMP combined with ablation of IL-35 facilitates increases NK cell proliferation and enhances NK cell dependent anti-tumor response. Further, we identify dysregulated transcriptional programs activated in pancreatic cancer-associated B cells that promote differentiation of naïve into immunosuppressive B cells and inhibit differentiation of anti-tumor plasma cells. The signaling network that contributes to this dysfunction is driven by IL35-mediated formation of STAT3-PAX5 complex that upregulates the transcriptional factor BCL6 in B cells. Transient inhibition of BCL6 in naïve B cells is sufficient to stimulate the intratumoral accumulation of plasma cells and effector T cells and renders pancreatic tumors sensitive to anti-PD-1 immune checkpoint blockade therapy. Our findings reveal that systemic STING signaling can expand immunosuppressive B cells and show that B cell differentiation can be re-routed towards anti-tumor plasma cell response, suggesting novel combinatorial strategies to facilitate anti-tumor immune activity. Citation Format: Yuliya Pylayeva-Gupta. Determinants of B cell fate and function in cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr IA016.
Abstract A077: PancreaCult™ Organoid Medium Kits support the robust establishment and expansion of human pancreatic duct organoids
Authors: Nina Quiskamp, Angela Tsai, Joanna Pan, Misha Hasan, George Chang, Isabella T. Tai, Allen C. Eaves, Sharon A. Louis, Ryan K. Conder
Journal: Cancer Research (2022)

Abstract Organoid culture is a novel in vitro culture method that promotes the growth of primary and PSC-derived cells in three-dimensional culture to generate structures that recapitulate tissue morphology. We have developed PancreaCult™ Organoid Medium Kits (Human), which combine PancreaCult™ Organoid Initiation Medium (OIM) and serum-free PancreaCult™ Organoid Growth Medium (OGM) into a robust and standardized workflow for the establishment and expansion of pancreatic duct organoids. To establish organoids, fresh or cryopreserved islet-depleted exocrine tissue was seeded in Corning® Matrigel® domes and cultured in PancreaCult™ OIM. After 3 days, the medium was changed to PancreaCult™ OGM and the organoids were passaged and maintained in this medium thereafter, and passaged as fragments every 4 - 7 days. Organoids were successfully established from all 5 donors with a 2- to 6-fold expansion in cell numbers every 7 - 14 days. Real-time PCR and immunocytochemistry demonstrated that these organoids express pancreatic duct markers (PDX1, SOX9, KRT19, CFTR, CA2, and MUC1), as well as proliferation and stem cell markers, Ki-67 and LGR5, respectively. Pancreatic duct organoids could be maintained for at least 10 passages (n = 3) and cryopreserved as fragments that could be used for rapid re-establishment of cultures at later time points. Organoids could also be dissociated and re-seeded in Prostaglandin E2-free PancreaCult™ OGM supplemented with ROCK inhibitor, Y-27632 and 10% FBS on Transwell® inserts to create 2D monolayers. In addition to normal pancreatic duct cultures, PancreaCult™ OGM supported the efficient long-term expansion of 4 pre-established pancreatic ductal adenocarcinoma (PDAC) organoid lines and maintained the mutational profile of the parent line after 5 passages, as determined through whole exome sequencing of 29 cancer-associated genes. Through the optional removal of epidermal growth factor (EGF), PancreaCult™ OGM can be modified to suppress normal cell growth to select for tumor cells with activating KRAS mutations. Our results demonstrate that PancreaCult™ Organoid Medium Kits provide a robust and flexible in vitro culture system for the establishment and expansion of normal pancreatic duct cells, as well as the long-term expansion of PDAC organoids. Citation Format: Nina Quiskamp, Angela Tsai, Joanna Pan, Misha Hasan, George Chang, Isabella T. Tai, Allen C. Eaves, Sharon A. Louis, Ryan K. Conder. PancreaCult™ Organoid Medium Kits support the robust establishment and expansion of human pancreatic duct organoids [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A077.
Abstract IA008: The origins and function of copy number alterations in pancreas cancer
Authors: Scott W. Lowe
Journal: Cancer Research (2022)

Abstract Pancreas ductal adenocarcinoma is a devastating disease that lacks effective treatment options. Often considered genetically homogenous, it is initiated by activation of oncogenic Kras and often sustains inactivating mutations in the TP53, CDKN2A, and SMAD4 tumor suppressor genes. However, additionally, advanced full blown PDAC often has a large degree of somatic copy number alterations (CNA) whose significance to disease etiology are poorly understood. Interestingly, gene mutations and copy number events may be interconnected, as TP53 mutations are strongly associated with the emergence of tumors harboring large number of CNAs, detectable chromothripsis, extensive intratumoral heterogeneity, and are often polyploid. Using new mouse modeling and genetic engineering approachs, we have begun to explore the emergence and functionality of copy number alterations in human PDAC. The current presentation will focus on the evolution of highly rearranged tumors that arise in Kras mutant pancreatic epithelial cells that sporadically inactivate p53, as well as the cell extrinsic functions of so-called CDKN2A deletions. The work highlights the fundamental importance of copy number events in PDAC. Citation Format: Scott W. Lowe. The origins and function of copy number alterations in pancreas cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr IA008.
Abstract A008: PanCAN SPARK: A cloud-based health data integration platform for pancreatic cancer data
Authors: Kawther Abdilleh, Omar Khalid, Dennis Ladnier, Wenshuai Wan, Sara Seepo, Garrett Rupp, Valentin Corelj, Zelia F. Worman, Bruce Press, Jack DiGiovanna, Satty Chandrashekhar, Eric Collisson, Karen Cui, Anirban Maitra, Paul A. Rejto, Kevin White, Lynn Matrisian, Sudheer Doss
Journal: Cancer Research (2022)

Abstract The Pancreatic Cancer Action Network (PanCAN) is leading large-scale research initiatives that will help transform the way pancreatic cancer is detected and treated including the Know Your Tumor precision medicine service, the Precision Promise adaptive clinical trial platform, the Early Detection Initiative, and the Patient Registry. Combined, these initiatives will generate a wide range of patient health data including molecular, multi-omic, clinical, patient-reported, treatment, outcomes, and imaging data. Here we introduce SPARK, a cloud-based data and analytics platform powered by Seven Bridges. SPARK integrates patient health data from PanCAN’s research initiatives and serves to accelerate research by making pancreatic cancer data easier to access and use. The platform supports the full spectrum of clinical data analysis with PanCAN patient health data as well as bioinformatics and analytical tools designed to leverage clinico-genomic data in a centralized location. SPARK fills an unmet need in pancreatic cancer research by providing researchers rapid and secure access to a wide range of pancreatic cancer patient health data on a platform backed by a robust cloud-based analytical infrastructure. The pilot release of the PanCAN SPARK platform brings qualified researchers closer to identifying novel treatments and ultimately improving patient outcomes. Citation Format: Kawther Abdilleh, Omar Khalid, Dennis Ladnier, Wenshuai Wan, Sara Seepo, Garrett Rupp, Valentin Corelj, Zelia F. Worman, Bruce Press, Jack DiGiovanna, Satty Chandrashekhar, Eric Collisson, Karen Cui, Anirban Maitra, Paul A. Rejto, Kevin White, Lynn Matrisian, Sudheer Doss. PanCAN SPARK: A cloud-based health data integration platform for pancreatic cancer data [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A008.